As Cherish Balls are obviously meant to be unavailable as a standalone item, and only used on event distributions, this question can be rephrased as "What games have a server-side hack check that's unfinished enough to take a look at the ball type and met location and still not immediately determine something's amiss from that?" Despite your desire not to bring up USUM and the adventures in Hoopa trading, that's exactly what's going on there: the server being apathetic enough not to speak up about these easily noticeable things.
Almost all Pokemon that were distributed in Cherish Balls also come with one of the event ribbons like the Wishing Ribbon as another distinguishing trait. In fact, these ribbons are what the game looks for, and if you attempt to send such a Pokemon over GTS or Wonder Trade, it will fail solely because of the ribbon. However, people have edited such Pokemon to remove the Ribbon while leaving the Cherish Ball intact, at which point the server lets them through just fine.
For what it's worth, the VGC rules have a clause explicitly banning any Pokemon that was hatched from an egg and that comes in a Cherish Ball or Master Ball (as those two ball types aren't inheritable, and become regular Poke Balls instead). However, it's something they have to check for manually, because the game logic isn't thorough enough to do the check itself and prevent the Pokemon from being registered in the first place.
